Homework 2 commentsSlide 2How Cells Decide Where to Go, What to Eat and What to Become: The Physics of Signaling and RegulationHow Cells Decide What to BecomeThe Development of the Operon Concept: What Cells Eat and When They DieGene Expression and the Central DogmaBut, Genes Are Precisely Controlled: Transcriptional RegulationRepressors: The CartoonActivators: The CartoonPowerPoint PresentationSlide 11The Lac Operon: The Hydrogen Atom of Gene RegulationThe Single Molecule CensusThe Notion of Fold-ChangeStatistical Mechanics of Promoter OccupancyReckoning Promoter OccupancyStatistical Mechanics of Polymerase Binding: Basal TranscriptionStatistical Mechanics of a Single Repressor Binding SiteExploring Regulatory DiversityHow Should We Think About Regulation Quantitatively?The Lambda Switch: The Other Hydrogen Atom of Gene RegulationBacteriophage and Their GenomesThe Life Cycle of Bacteriophage LambdaHomework 2 commentsHomework 2 commentsFrom R. Chisholm, Northwestern University.http://web.uct.ac.za/depts/mmi/jmoodie/flu2life.gifhttp://micro.magnet.fsu.edu/cells/viruses/influenzavirus.htmlHomework 2 commentsHomework 2 commentsFrom R. Chisholm, Northwestern University.QuickTime™ and aMicrosoft Video 1 decompressorare needed to see this picture.How Cells Decide Where to Go, What to Eat and What How Cells Decide Where to Go, What to Eat and What to Become: The Physics of Signaling and Regulationto Become: The Physics of Signaling and Regulation(Berman et al.)David RogersFrom R. Chisholm, Northwestern University.Neutrophils: life as a hunterFor the greater good: DictyosteliumNeutrophils cruise around looking for unwelcome invaders which they hunt and kill.When starved, amoeba can undertake a program to form a collective in which some of the cells are sacrificed.The bottom line: signaling, detection and decision making are central to cellular life.How Cells Decide What to BecomeHow Cells Decide What to Become(Berman et al.)From R. Chisholm, Northwestern University.QuickTime™ and aCinepak decompressorare needed to see this picture.Becoming a Sea UrchinAfter fertilization, sea urchin embryo undergoes a series of synchronized decisions and differentiation.Exquisite control in both space and time.The list of examples is virtually endless. Forming the GutThe Development of the Operon Concept: What Cells The Development of the Operon Concept: What Cells Eat and When They DieEat and When They Die(Berman et al.)The big idea: there are genes that control other genes!Bacterial growth curvesGene Expression and the Central Gene Expression and the Central DogmaDogmaThe central dogma tells us about the connection between what Crick dubbed “the two great polymer languages”. Gene expression refers to the chain of processes that relate the informational content of DNA to the protein consequences of that DNA.Managing the Great Polymer LanguagesBut, Genes Are Precisely Controlled: But, Genes Are Precisely Controlled: Transcriptional RegulationTranscriptional RegulationRegulation takes place very far upstream. In particular, the “decision” is made whether or not to produce mRNA.Question: What are the molecules that mediate this control?Repressors: The CartoonRepressors: The CartoonRepressor molecules inhibit action of RNA polymerase.Repressors can be under the control of other molecules (i.e. inducers) that dictate when repressor is bound and not.Activators: The CartoonActivators: The CartoonActivator molecules enhance the action of RNA polymerase.Activators can be under the control of other molecules (i.e. inducers) that dictate when activator is bound and not.Activators “RECRUIT” the polymerase.Adhesive interaction between RNAPand activatorBut quantitative data demands more than cartoons!Quantitative Measurement of Gene Quantitative Measurement of Gene Expression: When?Expression: When? (Elowitz and Leibler)Measurement of when genes are expressed.An example: the repressilator, a transcriptional regulatory network which leads to a time varying concentration of various gene products.The idea: stick an engineered set of genes into the cell and then turn them on.Quantitative Measurement of Gene Quantitative Measurement of Gene Expression: Where?Expression: Where? Developmental biology is one of the most compelling arenas for thinking about spacetime gene expression.(Davidson et al.)Fruit fly embryoSea urchin embryoBattle cry: quantitative measurements demand quantitative models!The Lac Operon: The Hydrogen Atom of The Lac Operon: The Hydrogen Atom of Gene RegulationGene Regulation “Tout ce qui est vrai pour le Colibacille est vrai pour l'éléphant.” MonodThe Single Molecule CensusThe Single Molecule Census(Beautiful work of David Goodsell)RNAP+DNA+mRNALac RepressorCRP and DNAProducts of the Lac OperonThe Notion of Fold-ChangeThe Notion of Fold-ChangeThe idea: by how many fold is the expression increased or decreased relative to some reference value.To measure fold-change one can measure the expression level (for example using fluorescent reporter molecules) for the case of interest and for the reference state.Statistical Mechanics of Promoter Statistical Mechanics of Promoter OccupancyOccupancyThe goal: compute the probability of promoter occupancy as a ratio of promoter occupied states to all of the states available to all of the polymerase molecules.Number of ways of arranging the polymerase molecules is a classic problem in statistics.Reckoning Promoter OccupancyReckoning Promoter OccupancyThe Outcome:We construct the ratio of weights for bound and unbound states.Statistical Mechanics of Polymerase Statistical Mechanics of Polymerase Binding: Basal TranscriptionBinding: Basal TranscriptionAction of transcription factors – the regulation factorKey insight: RNAP NOT bound in absence of helper molecules for ``normal’’ promoters.Freg accounts for the presence of regulatory proteins and features such as looping.106Statistical Mechanics of a Single Statistical Mechanics of a Single Repressor Binding SiteRepressor Binding SiteModel predicts concentration dependence of repression for a single repressor binding site.Extent of repression depends upon the strength of the binding site.Oehler et al.Vilar and LeiblerExploring Regulatory DiversityExploring Regulatory DiversityKey point: We can work out the regulation factor for many other scenarios including other looping scenarios.Synergistic ActivationBetter census needed!How Should We Think About Regulation How Should We Think
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